SMN2 Element 1 Antisense Compositions and Methods and Uses Thereof

ABSTRACT

The invention provides methods and compositions for treatment of spinal muscular atrophy (SMA). In one aspect of the invention, a series of compositions comprising an antisense oligonucleotide targeting the Element 1 site on the SMN2 pre-mRNA and a Morpholino backbone is disclosed. In another aspect of the invention, a method of treating SMA patients by modulating the splicing of SMN2 pre-mRNA to increase the amount of full-length SMN is disclosed. Certain embodiments of the inventive method comprise administering an E1-targeting antisense oligonucleotide, such as Morpholino based antisense oligonucleotide, to a SMA subject.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Application No.61/853,820, filed Apr. 12, 2013, which is incorporated herein byreference in its entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

This invention was made with Government support under Grant numberRO1NS041584 awarded by the National Institutes of Health. The Governmenthas certain rights in the invention.

INCORPORATION OF SEQUENCE LISTING

A Sequence Listing is contained in the file named “13UMC005_SEQLIST_ST25.txt” which is 4,245 bytes (measured in MS-Windows) andcomprising 24 nucleic acid sequences, created Apr. 10, 2014, iselectronically filed herewith and is incorporated herein by reference inits entirety.

FIELD OF INVENTION

The present invention relates to methods and compositions for treatingSpinal Muscular Atrophy (SMA), more specifically to a genetic therapybased on Element 1 antisense of SMN2 and Morpholino chemistry.

BACKGROUND OF INVENTION

Spinal Muscular Atrophies are collectively the second most commonautosomal recessive neurodegenerative group of disorders with anincidence of ˜1 in 6000 (Crawford, T. O. and Pardo, C. A., 1996) and acarrier frequency of ˜1 in 35 (Feldkotter, M. et al., 2002). Thediseases are caused by the loss of α-motor neurons resulting insubsequent atrophy of voluntary muscle groups leading to paralysis andeventually to premature infantile death. Genetically the types of SMAresult from a homozygous loss or mutation in the telomeric copy of theSurvival Motor Neuron-1 (SMN1) gene. All SMA patients rely on the nearlyidentical copy gene, SMN2, which produces low levels of functional SMNprotein. SMN is ubiquitously expressed and is a critical factor in avariety of RNA pathways. The best characterized SMN activity is in theassembly and maturation of the spliceosomal UsnRNPs (Meister, G., etal., 2002; Pellizzoni, L., et al., 2002). Even though the SMN2 gene is99% identical in nucleotide sequence and is completely identical inamino acid sequence, approximately 90% of SMN2-derived transcripts arealternatively spliced and encode a truncated protein lacking the finalcoding exon (exon 7). This aberrant splicing event is the result of asilent, non-polymorphic C to T nucleotide transition 6 nucleotideswithin exon 7 (Lorson, C. L., et al., 1999; Monani, U. R., et al.,1999). SMN2, however, is an excellent target for therapeuticintervention.

Cis-acting negative regulatory regions that surround SMN2 exon 7 havebeen identified and described (Lorson, C. L., et al., 1999; Miyaso, H.,et al., 2003; Miyajima, H., et al., 2002). In particular, ISS-N1 hasbeen a hotspot for experimental therapeutics, especially antisenseoligonucleotides (ASOs). ASO molecules of various lengths and backbonechemistries have been used to inhibit the repressor activity of ISS-N1,leading to an increase in SMN protein and significant extensions insurvival in animal models of SMA. For example, one such approach isdescribed in U.S. Pat. No. 8,110,560 B2 to Singh et al., which disclosesa series of oligonucleotide reagents that effectively target the SMN2ISS-NI site in the SMN2 pre-mRNA. U.S. Pat. No. 8,110,560 teaches thatthe ISS-N 1 blocking agents target the SMN2 pre-mRNA to modulate thesplicing of SMN2 to include exon 7. 2′-MOE chemistry has been used byISIS Pharmaceuticals in the development of their ASO, SMN-Rx (Hua, Y.,et al., 2011; Rigo, F., et al., 2012). Similar Morpholino-based ASOshave shown excellent pre-clinical promise in severe SMA mice and areunder further development.

Still, no effective treatment exists for SMA, and the complexity andexpansive clinical spectrum suggests that the SMA community cannotsolely rely upon a single lead compound or genetic target.

SUMMARY OF INVENTION

One aspect of the invention is drawn to a composition for blocking therepressive activity of the Element 1 of the SMN2 pre-mRNA. Such acomposition comprises an antisense oligonucleotide that comprises asequence annealing to a first region and a second region of the SMN2pre-mRNA. The first region is flanked by certain nucleotides, that is,the first region of the SMN2 pre-mRNA is defined by or consists of thenucleotides between −134 to −90 relative to exon 7 of the SMN2 pre-mRNA.The second region is flanked by certain nucleotides, that is, the secondregion of the SMN2 pre-mRNA is defined by or consists of the nucleotidesbetween −105 to −45 relative to exon 7 of the SMN2 pre-mRNA. In certainembodiments, the antisense oligonucleotide comprises or consists of anucleic acid sequence selected from the group consisting of SEQ ID NO:17 (v1.11), SEQ ID NO: 16 (v1.10), SEQ ID NO: 6 (v1.00), SEQ ID NO: 7(v1.01), SEQ ID NO: 8 (v1.02), SEQ ID NO: 9 (v1.03), SEQ ID NO: 10(v1.04), SEQ ID NO: 11 (v1.05), SEQ ID NO: 12 (v1.06), SEQ ID NO: 13(v1.07), SEQ ID NO: 14 (v1.08). SEQ ID NO: 15 (v1.09), and SEQ ID NO: 18(v1.12).

In certain embodiments, the antisense oligonucleotide comprises anucleotide sequence that is complementary to at least eight consecutivenucleotides of the first region of the SMN2 pre-mRNA and iscomplementary to at least eight consecutive nucleotides of the secondregion of the SMN2 pre-mRNA. In certain embodiments, the sequence of theantisense oligonucleotide that is complementary to the second region ofthe SMN2 pre-mRNA is 5′ of the sequence of the antisense nucleotide thatis complementary to the first region of the SMN2 pre-mRNA.

In certain embodiments, the antisense oligonucleotide is not entirelycomplementary to the SMN2 pre-mRNA and contains one or moresubstitutions. For example in certain embodiments, the antisenseoligonucleotide comprises:

i. a nucleotide sequence that is complementary to, except for having oneor two nucleotide substitutions, at least eight consecutive nucleotidesof the first region of the SMN2 pre-mRNA and is complementary to atleast eight consecutive nucleotides of the second region of the SMN2pre-mRNA;

ii. a nucleotide sequence that is complementary to at least eightconsecutive nucleotides of the first region of the SMN2 pre-mRNA andthat is complementary, except for having one or two nucleotidesubstitutions, to at least eight consecutive nucleotides of the secondregion of the SMN2 pre-mRNA; or

iii. a nucleotide sequence that is complementary to, except for havingone or two nucleotide substitutions, at least eight consecutivenucleotides of the first region of the SMN2 pre-mRNA and that iscomplementary, except for having one or two nucleotide substitutions, toat least eight consecutive nucleotides of the second region of the SMN2pre-mRNA.

In certain embodiments, the antisense oligonucleotide comprises anucleic acid sequence selected from the group consisting of SEQ ID NO:17 (v1.11), SEQ ID NO: 16 (v1.10), SEQ ID NO: 6 (v1.00), SEQ ID NO: 7(v1.01), SEQ ID NO: 11 (v1.05), SEQ ID NO: 12 (v1.06), SEQ ID NO: 13(v1.07), SEQ ID NO: 14 (v1.08). SEQ ID NO: 15 (v1.09), and SEQ ID NO: 18(v1.12).

Certain aspects of the invention are drawn to methods for blocking therepressive activity of the Element 1 of the SMN2 pre-mRNA. In certainembodiments, such a method comprises administrating to a subject acomposition for blocking the repressive activity of the Element 1 of theSMN2 pre-mRNA of the invention.

Certain aspects of the invention are drawn to methods for treatingSpinal Muscular Atrophy (SMA) in a human SMA patient. In certainembodiments, such a method comprises the step of administrating to thepatient an effective amount of a composition for blocking the repressiveactivity of the Element 1 of the SMN2 pre-mRNA of the invention.

Certain aspects of the invention are drawn to a composition for blockingthe repressive activity of the Element 1 of the SMN2 pre-mRNA, whereinthe compositions comprising an antisense oligonucleotide with a sequenceannealing to a first region and a second region of the SMN2 pre-mRNA andwherein the first region consists of the nucleotides between −134 to−120 relative to exon 7 of the SMN2 pre-mRNA and the second regionconsists of the nucleotides between −67 to −54 relative to exon 7 of theSMN2 pre-mRNA.

Certain aspects of the invention are drawn to methods for blocking therepressive activity of the Element 1 of the SMN2 pre-mRNA, therebymodulating the splicing pattern of the SMN2 to generate full-length(exon-7-retaining) SMN comprising the step of administrating to asubject a composition comprising an antisense nucleotide with a sequenceannealing to two distinct regions flanking E1 on the SMN2 pre-mRNA,whereas the regions consist of the nucleotides between −134 to −120 and−67 to −54 (relative to exon 7).

In one aspect of the invention, a series of compositions capable ofblocking or inhibiting the repressive activity of the SMN2 splicesilencing domain, Element 1 (El), is described. In certain embodiments,the inventive E1 antisense oligonucleotide (ASO) anneals to two distinctregions of two distinct regions of the SMN2 pre-mRNA (intron 6sequence), and in certain embodiments, relative to exon 7 of the SMN2pre-mRNA, the inventive ASO anneals to: −134 to −120 and −67 to −54. Incertain embodiments, the backbone for the inventive E1 ASO comprisesMorphonlino residues.

In another aspect of the invention, a method of treating spinal muscularatrophy (SMA) in a subject is described. In certain embodiments, theinventive method for treating SMA comprises the step of administering toa subject an E1 ASO described herein in a dose effective to enhance thelevel of exon 7-containing SMN2 mRNA in cells of the subject.

In any of the compositions or methods herein, the antisenseoligonucleotide can comprise a Morpholino backbone.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic illustration of the location of Element 1 relativeto Exon 7 of the SMN2 pre-mRNA and an exemplary antisenseoligonucleotide according to one embodiment of the invention.

FIG. 2 is a sequence alignment showing the sequences of SEQ ID NOs: 6-18complementary to the SMN2 pre-mRNA −133 to −46 region upstream of intron7.

FIG. 3 shows weight gains among treated mice and controls in Example 1.

FIG. 4 shows survival among treated mice and controls in Example 1.

FIG. 5 is a bar graph summarizing the weight gains among treated miceand controls in Example 2.

FIG. 6 is a bar graph summarizing the “Time to Right” motor functiontest among treated mice and controls in Example 2.

FIG. 7 is a graph summarizing the grip strength motor function testamong treated mice and controls in Example 2.

FIG. 8 is a graph summarizing the Rota-rod performance test betweentreated mice and the wild controls in Example 2.

FIG. 9 is a graph summarizing the survival data among treated mice andvarious controls in Example 2.

FIG. 10 is an array and Western Blot analysis on protein induction amongthe treated mice and controls in Example 2.

FIG. 11 is a quantitative graph for the Western Blot analysis in Example2.

FIG. 12 a shows the RT-PCR analysis for SMN-full length and SMNA7 levelsin the cells of treated mice and controls in Example 2.

FIG. 12 b is a quantitative graph for SMN-full length and SMNA7 levelsin the cells of the treated mice and controls in Example 2.

FIG. 13 illustrates targeting of the intronic repressor Element 1 withantisense oligonucleotides versus previously published ASO sequencestargeting the intronic silencer ISS-N1.

FIG. 14 shows an increase in full-length SMN transcript afterE1^(MO)-ASO treatment in Example 3.

FIG. 15 shows that injection of morpholino based ASO targeting theElement1 repressor increased total SMN protein in the Δ7SMA mouse modelin Example 3.

FIG. 16 a shows that severe SMNΔ7 SMA mice showed significantimprovement in survival and longevity after injections with E1^(MO)-ASOoligos in Example 3.

FIG. 16 b shows survival curves demonstrating a significant increase inlife expectancy for E1^(MO)-ASO ICV, ICV&ICV and ICV&IP injected animalsin Example 3.

FIG. 17 shows that E1^(MO)-ASO treatment results in a significant weightgain in Example 3.

FIG. 18 a shows the percent weight gained from birth to peak was alsocompared between groups treated in Example 3.

FIG. 18 b shows statistical significance between each treatment group inFIG. 18 a.

FIG. 19 shows individual weights on P12 for all controls and animalstreated with E1^(MO)-ASO in Example 3.

FIG. 20 is a bar graph showing the percent of all tested animal groupsable to right themselves from a prone position in Example 3.

FIG. 21 a is a graph representing raw data of the average time to rightfrom P7 to P25 in Example 3.

FIG. 21 b is a scatter plot of TTR performance of mice injected withE1^(MO)-ASO in Example 3.

FIG. 22 shows grip strength measurements in grams in Example 3.

FIG. 23 shows results of the rotarod performance test in Example 3.

FIG. 24 a is a Western blot (n=3) showing increased SMN in spinal cordtissue of five (5) ICV injected animals with E1^(MO)-ASO in Example 3.

FIG. 24 b shows Western blot quantification of FIG. 24 a.

FIG. 25 shows that the treated SMN^(RT) animals (labeled “SMN^(RT)E1^(MO)-ASO”) and the unaffected littermates (labeled “SMN^(RT)Unaffected”) were substantially more vigorous and lived more than 180days compared to the untreated mice (labeled “SMA^(RT) Untreated”) inExample 3.

FIG. 26 shows a significant increase in the average weight of SMN^(RT)animal model after treatment with E1^(MO)-ASO in Example 3.

FIG. 27 show a comparison of the percent weight gained from birth topeak between animal groups in Example 3.

FIG. 28 shows individual weights on P12 in Example 3.

FIG. 29 shows the percent of the tested animals able to right themselvescompared to untreated mice where the TTR reflex is delayed in Example 3.

FIG. 30 shows the average time to right from P7 to P25 for allexperimental groups in Example 3.

FIG. 31 is a scatter plot of TTR performance of SMN^(RT) mice injectedwith E1^(MO)-ASO in Example 3.

FIG. 32 shows grip strength measurements in grams in Example 3.

FIG. 33 shows results of the rotarod performance test in Example 3.

FIG. 34 is RT-PCR quantification showing the percent increase in fulllength SMN transcript in three SMA animals after treatment withE1^(MO)-ASO in Example 3.

FIG. 35 is Western blot quantification showing the percent increase inSMN protein induction was compared to the unaffected and untreatedcontrol group and plotted in a bar graph (n=5) in Example 3.

DESCRIPTION OF THE SEQUENCES

Illustrative examples of sequences useful in certain embodiments of theinvention, including antisense oligo sequences targeting the E1repressor include, but are not limited to, the following:

1. SEQ ID NO: 1 is a partial Intron 6 sequence containing the entireElement 1 (−112; −67):

(SEQ ID NO: 1) 5′-TGCAAGAAAACCTTAACTGCAGCCTAATAATTGTTTTCTTTGGGATAACTTTTAAAGTACATTAAAAGACTATCAACTTAATTTCTGATCATATTTTGTTGAATAAAATAAGTAAAATGTCTTGTGAAACAAAATGCTTTTTAACATCCATATAAAGCTATCTATATATAGCTATCTATGTCTATATAGCTATTTTTTTTAACTTCCTTTATTTTCCTTACA [EXON7]-3′2. SEQ ID NO: 2 is the Miaso 45-mer Element 1 (−112; −67) within Intron6:

(SEQ ID NO: 2) 5′-(112)GTAAAATGTCTTGTGAAACAAAATGCTTTTTAACATCCATATAAA(67)-3′ (Miaso 45-mer; bold within SEQ ID NO: 1 above)3. SEQ ID NO: 3 is a partial sequence of SEQ ID NO: 1 comprising E1flanking regions shown in bold:

(SEQ ID NO: 3) 5′-(134)ATATTTTGTTGAATAAAATAAGTAAAATGTCTTGTGAAACAAAATGCTTTTTAACATCCATATAAAGCTATCTATATATAGCTATC T(54)-3′4. SEQ ID NO: 4 is the reverse of SEQ ID NO: 3 (i.e, SEQ ID NO: 3 shown3′ to 5′):

(SEQ ID NO: 4) 3′-TCTATCGATATATATCTATCGAAATATACCTACAATTTTTCGTAAAACAAAGTGTTCTGTAAAATGAATAAAATAAGTTGTTTTATA-5′5. SEQ ID NO: 5 is an ASO-based bifunctional (BiF) RNA targeting the E1repressor:

(SEQ ID NO: 5) 5′-CTATATATAGATAGTTATTCAACAAAACTAGTAATTTTT-3′6. SEQ ID NO: 6 is a 26-mer antisense sequence targeting the E1repressor referred to herein as “Element 1 v1.00 ASO”:

(SEQ ID NO: 6; v1.00) 5′-CTATATATAGATAGTTATTCAACAAA-3′7. SEQ ID NO: 7 is a 25-mer antisense sequence targeting the E1repressor referred to herein as “Element 1 v1.01 ASO”:

(SEQ ID NO: 7; v1.01) 5′-TAGATAGCTTTACATTTTACTTATT-3′8. SEQ ID NO: 8 is a 25-mer antisense sequence targeting the E1repressor referred to herein as “Element 1 v1.02 ASO”:

(SEQ ID NO: 8; v1.02) 5′-TATGGATGTTAAAAAGCATTTTGTT-3′9. SEQ ID NO: 9 is a 25-mer antisense sequence targeting the E1repressor referred to herein as “Element 1 v1.03 ASO”:

(SEQ ID NO: 9; v1.03) 5′-CTATATATAGATAGCTTTATATGGA-3′10. SEQ ID NO: 10 is a 25-mer antisense sequence targeting the E1repressor referred to herein as “Element 1 v1.04 ASO”:

(SEQ ID NO: 10; v1.04) 5′-CATTTTACTTATTTTATTCAACAAA-3′11. SEQ ID NO: 11 is a 25-mer antisense sequence targeting the E1repressor referred to herein as “Element 1 v1.05 ASO”:

(SEQ ID NO: 11; v1.05) 5′-GCTTTATATGGACATTTTACTTATT-3′12. SEQ ID NO: 12 is a 25-mer antisense sequence targeting the E1repressor referred to herein as “Element 1 v1.06 ASO”:

(SEQ ID NO: 12; v1.06) 5′-GATGTTAAAAAGCGTTTCACAAGAC-3′13. SEQ ID NO: 13 is a 25-mer antisense sequence targeting the E1repressor referred to herein as “Element 1 v1.07 ASO”:

(SEQ ID NO: 13; v1.07) 5′-TATATGGATGTTATTATTCAACAAA-3′14. SEQ ID NO: 14 is a 25-mer antisense sequence targeting the E1repressor referred to herein as “Element 1 v1.08 ASO”:

(SEQ ID NO: 14; v1.08) 5′-GCATTTTGTTTCACAAGTTATTCAA-3′15. SEQ ID NO: 15 is a 25-mer antisense sequence targeting the E1repressor referred to herein as “Element 1 v1.09 ASO”:

(SEQ ID NO: 15; v1.09) 5′-CTATATATAGATAGCGACATTTTAC-3′16. SEQ ID NO: 16 is a 26-mer antisense sequence targeting the E1repressor referred to herein as “Element 1 v1.10 ASO”:

(SEQ ID NO: 16; v1.10) 5′-AGATAGCTTTATATGGATTTATTCAA-3′17. SEQ ID NO: 17 is a 20-mer antisense sequence targeting the E1repressor referred to herein as “Element 1 v1.11 ASO”:

(SEQ ID NO: 17; v1.11) 5′-CTATATATAGTTATTCAACA-3′18. SEQ ID NO: 18 is a 24-mer antisense sequence targeting the E1repressor referred to herein as “Element 1 v1.12 ASO”:

(SEQ ID NO: 18; v1.12) 5′-TTTATATGGATGAAGACATTTTAC-3′19. SEQ ID NO: 19 is a mSmn-WT forward primer:

(SEQ ID NO: 19) 5′-tctgtgttcgtgcgtggtgacttt-3′20. SEQ ID NO: 20 is a mSmn-WT reverse primer:

(SEQ ID NO: 20) 5′-cccaccacctaagaaagcctcaat-3′21. SEQ ID NO: 21 is a Smn knockout SMN1-KO forward primer:

(SEQ ID NO: 21) 5′-ccaacttaatcgccttgcagcaca-3′22. SEQ ID NO: 22 is a Smn knockout SMN1-KO reverse primer:

(SEQ ID NO: 22) 5′-aagcgagtggcaacatggaaatcg-3′23. SEQ ID NO: 23 is a negative scrambled control:

(SEQ ID NO: 23) 5′-CCU CUU ACC UCA GUU ACA AUU UAU A-3′24. SEQ ID NO: 24 is a E1^(MO)-ASO (26-mer):

(SEQ ID NO: 24) 5′-CUA UAU AUA GAU AGU UAU UCA ACA AA-3′

DETAILED DESCRIPTION

Spinal muscular atrophy (SMA) is a neurodegenerative disease caused bythe loss of Survival Motor Neuron-1 (SMN1) (SMN1=survival of motorneuron 1, telomeric [Homo sapiens] GenBank accession numberNG_(—)008691.1 (Genomic); NC_(—)000005.10 (Chromosome);NM_(—)000344.3--->NP_(—)000335.1 (mRNA & Protein)). In all SMA patientsa nearly identical copy gene called SMN2 is present which produces lowlevels of functional protein due to an alternative splicing event(SMN2=survival of motor neuron 2, centromeric [Homo sapiens] GenBankaccession number NG_(—)008728.1 (Genomic); NC_(—)000005.10 (Chromosome);NM_(—)017411.3--->NP_(—)059107.1 (mRNA & Protein)).

Without being bound by theory, certain aspects of the invention aredrawn to preventing exon-skipping by targeting an intronic repressor,SMN2 Element 1 (E1), located upstream (5′-) of SMN2 exon 7 (FIG. 1). Incertain embodiments, E1 and/or regions upstream (5′-) and/or downstream(3′-) of E1 are targeted using compositions comprisingantisense-oligonucleotides (referred to herein generally as E1-ASOs)(illustrative examples shown in FIG. 2). Certain embodiments are drawnto compositions for blocking or inhibiting the repressive activity ofthe Element E1 of the SMN2 pre-mRNA wherein the composition comprises anantisense oligonucleotide. It is understood that a compositioncomprising an antisense oligonucleotide could consist or essentiallyconsist of an antisense oligonucleotide such that certain embodimentsare drawn to antisense oligonucleotides for blocking or inhibiting therepressive activity of the Element E1 of the SMN2 pre-mRNA. As usedherein, “blocking” or “inhibiting” is used to describe the process oflimiting and/or preventing the repressor function of SMN2 Element 1. Incertain embodiments, any of the antisense oligonucleotides describedherein are Morpholino-based antisense oligonucleotides (referred toherein generally as E1^(MO)-ASOs). Morpholino oligonucleotides, asreferred to herein, comprise morpholine rings in their backbones, whichreplace the ribose or deoxyribose rings characteristic of RNA and DNAoligonucleotides. Morpholinos contain uncharged phosphorodiamidateinter-subunit linkages instead of the anionic phosphodiester linkagefound in natural nucleic acids. The morpholine rings carry A, C, G or Tbases positioned suitably for Watson-Crick base pairing.

SMN2 Element 1 (E1) has been previously explored by characterizing thegenetic region upstream of SMN2 exon 7 as a repressor of SMN2 exon 7inclusion. The genetic activity of E1 reduces the production of thefull-length SMN product by promoting the exclusion of exon 7 and theexpression of the truncated isoform (SMN-delta 7). 2′-O-Methyl ASO-basedbifunctional (BiF) RNAs have been tested that target the E1 repressorand with ICV injection extended survival by ˜48 hours. BiF RNAs areASO-like molecules that derive their name from the presence of twofunctional domains: an RNA sequence that is an antisense elementcomplementary to a specific cellular RNA (e.g. SMN Intron 6, Exon 7, orIntron 7); and an untethered RNA segment that serves as asequence-specific binding platform for cellular splicing factors, suchas SR proteins. The 5′ end of exon 7 was targeted with the antisenseelement; however, it is possible that an antisense sequence within exon7 does not allow for proper recognition of the necessary splicingsignals. To enhance the activity of the SMN bifunctional RNAs, a set ofRNAs that targeted El and ISS-N1 were developed. By targeting arepressor sequence with the anti-sense sequence, there was a 2-foldmechanism of SMN induction: inhibition of the intronic repressor andrecruitment of SR proteins via the SR recruitment sequence of thebifunctional RNA. Based upon molecular understanding of SMN exon 7regulation, high affinity binding sites for hTra21 or SF2/ASF—twofactors known to stimulate exon 7 inclusion were incorporated. However,the 2′-O-Methyl chemistry used in these experiments has proven to besuboptimal for in vivo activity.

Antisense oligonucleotides targeting the E1 region and/or surroundingregions of SMN2 (i.e., distinct from targeting ISS-N1) have beendeveloped and examined in two important animal models of disease: the“gold standard” SMN17 mouse, which is a very severe model living only˜14 days; and a recently developed model called SMN^(RT), in whichanimals live ˜35 days and represent a less severe population. Work wasdone in transgenic mouse that has the human SMN2 gene. All data herein(e.g., RNA, protein, etc.) represent the human SMN2 gene in a mouse withthe mouse Smn gene deleted (Smn1=survival motor neuron 1 [Mus musculus(house mouse)] GenBank accession number NT_(—)187006.1 (Genomic);NC_(—)000079.6 (Chromosome); NM_(—)011420.2→NP_(—)035550.1 survivalmotor neuron protein isoform 1 (mRNA & Protein)NM_(—)001252629.1→NP_(—)001239558.1 survival motor neuron proteinisoform 2 (mRNA & Protein)). Therefore, in certain embodiments,antisense oligonucleotides are targeted to the human SMN2 gene.

It has been discovered that using a relatively low dose of certainElement 1 Morpholino ASOs (E1^(MO)-ASOs), the SMA phenotype at themolecular, cellular, and organismal levels were largely rescued,including a 300-700% extension in survival for the two mouse models.From a pre-clinical perspective, there is excellent target engagement(SMN2 splicing), molecular efficacy (SMN protein production), and robustphenotypic rescue in two complementary models of disease. Collectively,this work identifies lead ASO candidates that target a distinct regionof the SMN2 pre-mRNA.

Representative embodiments of the invention are directed to new methodsand compositions based on Antisense Oligonucleotides (ASOs) technologyand Morpholino chemistry for modulating the SMN2 splicing pattern togenerate increased levels of exon 7-containing full-length SMN. Incertain embodiments, the increased level of exon 7-containingfull-length SMA is sufficient to provide a viable therapy to SpinalMuscular Atrophy (SMA) patients. Certain embodiments comprise a seriesof compositions capable of blocking or inhibiting the repressiveactivity of the SMN2 splice silencing domain, Element 1 (E1). Forexample, certain embodiments comprise E1 antisense oligonucleotide basedcompositions that block or inhibit the splice inhibitory effects of theE1, thereby modulating splicing of the SMN2 pre-mRNA to generate exon 7retaining full-length SMN.

In certain embodiments, a composition comprises an E1 antisenseoligonucleotide (E1-ASO) with a sequence annealing to two distinctregions flanking E1 on the SMN2 pre-mRNA, wherein the regions comprisethe nucleotides between −134 to −120 and −67 to −54 (relative to exon7). In certain embodiments, such E1-ASO further comprises a Morpholinobackbone.

FIG. 1 illustrates an exemplary E1-ASO. As shown in FIG. 1, the E1-ASOis designed with two split antisense sequences annealing to two regionsflanking repressor E1: Region (67-54) and Region (134-120). To increaseexon 7-containing SMN expression, a two-pronged strategy to design theantisense may be used: on one side includes two antisense regions thatblock E1 and on the other end a sequence that recruits exonic spliceenhancers specific for exon 7.

Other embodiments can incorporate additional antisense oligonucleotidesannealing to the sequences on either side of the two regions—i.e.,Region (−67 to −54) and Region (−134 to −120)—and/or sequences within orpartially within the E1 motif. FIG. 2 is an alignment (sequences shownreversed, i.e., 3′ to 5′) of the region comprising the nucleotides −46to −133 that are 5′ (upstream) of SMN2 Exon 7, including the E1 motif(italicized nucleotides), and showing in bold underline the sequences ofthe region of the SMN2 pre-mRNA complementary to the antisenseoligonucleotide sequences of SEQ ID NOs: 6 to 18, i.e., v1.00 to v.1.12,respectively.

Certain embodiments are drawn to compositions comprising an antisenseoligonucleotide that comprises a nucleotide sequence that anneals to theregion comprising nucleotides −46 to −133 that are 5′ (upstream) of SMN2Exon 7. In certain embodiments, the antisense oligonucleotide comprisesa sequence that anneals to two regions of the nucleotides −46 to −133that are 5′ (upstream) of SMN2 Exon 7, wherein the first regioncomprises the nucleotides between −134 to −90 relative to exon 7 of theSMN2 pre-mRNA and the second region comprises the nucleotides between−105 and −45 relative to exon 7 of the SMN2 pre-mRNA. In order for anantisense oligonucleotide targeting the E1 region to modulate theactivity of Element 1, it is understood that “anneal(s)” or “annealing,”as used herein, refers to annealing of two substantially complementarynucleic acid molecules under physiological conditions. In certainembodiments, the first region comprises: the nucleotides between −134 to−90; the nucleotides between −134 to −95; the nucleotides between −134to −100; the nucleotides between −134 to −105; the nucleotides between−134 to −110; or the nucleotides between −134 to −115, relative to exon7 of the SMN2 pre-mRNA. In certain embodiments, the second regioncomprises: the nucleotides between −90 to −45; the nucleotides between−85 to −45; the nucleotides between −80 to −45; the nucleotides between−75 to −45; the nucleotides between −70 to −45; or the nucleotidesbetween −65 to −45, relative to exon 7 of the SMN2 pre-mRNA. In certainembodiments, the first and/or second regions consist of any of the abovedefined regions upstream of exon 7 of the SMN2 pre-mRNA. In certainembodiments the first and second regions of the SMN2 pre-mRNA are acombination of any of the above first and second regions, for examplethe first region comprises the nucleotides between −134 to −95 and thesecond region comprises the nucleotides between −85 to −45, for examplethe first region comprises the nucleotides between −134 to −115 and thesecond region comprises the nucleotides between −65 to −45, etc.

In certain embodiments, the antisense oligonucleotide sequence comprisesa certain number of nucleotides that are complementary to consecutivenucleotides of the region comprising the nucleotides −46 to −133 thatare 5′ (upstream) of SMN2 Exon 7. In certain embodiments, the antisenseoligonucleotide comprises a nucleotide sequence that is complementary toat least 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, or 26 consecutive nucleotides of the region comprisingnucleotides −46 to −133 that are 5′ (upstream) of SMN2 Exon 7. Incertain embodiments, the antisense oligonucleotide comprising anucleotide sequence that is complementary to at least 6, 7, 8, 9, 10,11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26consecutive nucleotides of the region comprising nucleotides −46 to −133that are 5′ (upstream) of SMN2 Exon 7 is not entirely complementary andcomprises one, two, three, four, five, or six nucleotide substitutionsin the antisense oligonucleotide sequence. In certain embodiments, theantisense oligonucleotide comprises a nucleotide sequence that iscomplementary to at least 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15consecutive nucleotides of any of the first regions listed herein. Incertain embodiments, the antisense oligonucleotide comprising anucleotide sequence that is complementary to at least 6, 7, 8, 9, 10,11, 12, 13, 14, or 15 consecutive nucleotides of any of the firstregions listed herein is not entirely complementary and comprises one,two, three, four, five, or six, nucleotide substitutions in theantisense oligonucleotide sequence. In certain embodiments, theantisense oligonucleotide comprises a nucleotide sequence that iscomplementary to at least 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15consecutive nucleotides of any of the second regions listed herein. Incertain embodiments, the antisense oligonucleotide comprising anucleotide sequence that is complementary to at least 6, 7, 8, 9, 10,11, 12, 13, 14, or 15 consecutive nucleotides of any of the secondregions listed herein is not entirely complementary and comprises one,two, three, four, five, or six, nucleotide substitutions in theantisense oligonucleotide sequence. In certain embodiments, theantisense oligonucleotide comprises a nucleotide sequence that iscomplementary to at least 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15consecutive nucleotides of any of the first regions listed herein andcomplementary to at least 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15consecutive nucleotides of any of the second regions listed herein. Incertain embodiments, the antisense oligonucleotide comprising anucleotide sequence that is complementary to at least 6, 7, 8, 9, 10,11, 12, 13, 14, or 15 consecutive nucleotides of any of the firstregions listed herein and complementary to at least 6, 7, 8, 9, 10, 11,12, 13, 14, or 15 consecutive nucleotides of any of the second regionslisted herein is not entirely complementary and comprises one, two,three, four, five, or six, nucleotide substitutions in the antisenseoligonucleotide sequence. In certain embodiments, the antisenseoligonucleotide comprises a nucleotide sequence that is complementary toat least eight consecutive nucleotides of any of the first regionslisted herein. In certain embodiments, the antisense oligonucleotidecomprises a nucleotide sequence that is complementary to at least eightconsecutive nucleotides of any of the second regions listed herein. Incertain embodiments, the antisense oligonucleotide comprises anucleotide sequence that is complementary to at least eight consecutivenucleotides of any of the first regions listed herein and complementaryto at least eight consecutive nucleotides of any of the second regionslisted herein. In the SMN2 pre-mRNA, the first regions listed herein areupstream (5′) of the second regions listed herein. In the antisenseoligonucleotide sequences, however, the nucleotide sequence of theantisense oligonucleotide that is complementary to the second region ofthe SMN2 pre-mRNA is upstream (5′) of the nucleotide sequence of theantisense oligonucleotide that is complementary to the first region ofthe SMN2 pre-mRNA.

Certain embodiments are drawn to compositions comprising an antisenseoligonucleotide that comprises a nucleotide sequence that anneals to theregion consisting of nucleotides −46 to −133 that are 5′ (upstream) ofSMN2 Exon 7. In certain embodiments, the antisense oligonucleotidecomprises a sequence that anneals to two regions of the nucleotides −46to −133 that are 5′ (upstream) of SMN2 Exon 7, wherein the first regionconsists of the nucleotides between −134 to −90 relative to exon 7 ofthe SMN2 pre-mRNA and the second region consists of the nucleotidesbetween −105 and −45 relative to exon 7 of the SMN2 pre-mRNA. In orderfor an antisense oligonucleotide targeting the E1 region to modulate theactivity of Element 1, it is understood that “anneal(s)” or “annealing,”as used herein, refers to annealing of two substantially complementarynucleic acid molecules under physiological conditions. In certainembodiments, the first region consists of: the nucleotides between −134to −90; the nucleotides between −134 to −95; the nucleotides between−134 to −100; the nucleotides between −134 to −105; the nucleotidesbetween −134 to −110; or the nucleotides between −134 to −115, relativeto exon 7 of the SMN2 pre-mRNA. In certain embodiments, the secondregion consists of: the nucleotides between −90 to −45; the nucleotidesbetween −85 to −45; the nucleotides between −80 to −45; the nucleotidesbetween −75 to −45; the nucleotides between −70 to −45; or thenucleotides between −65 to −45, relative to exon 7 of the SMN2 pre-mRNA.In certain embodiments, the first and/or second regions consist of anyof the above defined regions upstream of exon 7 of the SMN2 pre-mRNA. Incertain embodiments the first and second regions of the SMN2 pre-mRNAare a combination of any of the above first and second regions, forexample the first region consists of the nucleotides between −134 to −95and the second region consists of the nucleotides between −85 to −45,for example the first region consists of the nucleotides between −134 to−115 and the second region consists of the nucleotides between −65 to−45, etc.

In certain embodiments, the antisense oligonucleotide sequence comprisesa certain number of nucleotides that are complementary to consecutivenucleotides of the region consisting of the nucleotides −46 to −133 thatare 5′ (upstream) of SMN2 Exon 7. In certain embodiments, the antisenseoligonucleotide comprises a nucleotide sequence that is complementary toat least 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, or 26 consecutive nucleotides of the region consisting ofnucleotides −46 to −133 that are 5′ (upstream) of SMN2 Exon 7. Incertain embodiments, the antisense oligonucleotide comprising anucleotide sequence that is complementary to at least 6, 7, 8, 9, 10,11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26consecutive nucleotides of the region consisting of nucleotides −46 to−133 that are 5′ (upstream) of SMN2 Exon 7 is not entirely complementaryand comprises one, two, three, four, five, or six nucleotidesubstitutions in the antisense oligonucleotide sequence. In certainembodiments, the antisense oligonucleotide comprising a nucleotidesequence that is complementary to at least 6, 7, 8, 9, 10, 11, 12, 13,14, or 15 consecutive nucleotides of any of the first regions listedherein. In certain embodiments, the antisense oligonucleotide comprisinga nucleotide sequence that is complementary to at least 6, 7, 8, 9, 10,11, 12, 13, 14, or 15 consecutive nucleotides of any of the firstregions listed herein is not entirely complementary and comprises one,two, three, four, five, or six, nucleotide substitutions in theantisense oligonucleotide sequence. In certain embodiments, theantisense oligonucleotide comprises a nucleotide sequence that iscomplementary to at least 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15consecutive nucleotides of any of the second regions listed herein. Incertain embodiments, the antisense oligonucleotide comprising anucleotide sequence that is complementary to at least 6, 7, 8, 9, 10,11, 12, 13, 14, or 15 consecutive nucleotides of any of the secondregions listed herein is not entirely complementary and comprises one,two, three, four, five, or six, nucleotide substitutions in theantisense oligonucleotide sequence. In certain embodiments, theantisense oligonucleotide comprises a nucleotide sequence that iscomplementary to at least 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15consecutive nucleotides of any of the first regions listed herein andcomplementary to at least 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15consecutive nucleotides of any of the second regions listed herein. Incertain embodiments, the antisense oligonucleotide comprising anucleotide sequence that is complementary to at least 6, 7, 8, 9, 10,11, 12, 13, 14, or 15 consecutive nucleotides of any of the firstregions listed herein and complementary to at least 6, 7, 8, 9, 10, 11,12, 13, 14, or 15 consecutive nucleotides of any of the second regionslisted herein is not entirely complementary and comprises one, two,three, four, five, or six, nucleotide substitutions in the antisenseoligonucleotide sequence. In certain embodiments, the antisenseoligonucleotide comprises a nucleotide sequence that is complementary toat least eight consecutive nucleotides of any of the first regionslisted herein. In certain embodiments, the antisense oligonucleotidecomprises a nucleotide sequence that is complementary to at least eightconsecutive nucleotides of any of the second regions listed herein. Incertain embodiments, the antisense oligonucleotide comprises anucleotide sequence that is complementary to at least eight consecutivenucleotides of any of the first regions listed herein and complementaryto at least eight consecutive nucleotides of any of the second regionslisted herein. In the SMN2 pre-mRNA, the first regions listed herein areupstream (5′) of the second regions listed herein. In the antisenseoligonucleotide sequences, however, the nucleotide sequence of theantisense oligonucleotide that is complementary to the second region ofthe SMN2 pre-mRNA is upstream (5′) of the nucleotide sequence of theantisense oligonucleotide that is complementary to the first region ofthe SMN2 pre-mRNA.

In certain embodiments, while the antisense oligonucleotide anneals toand/or comprises a nucleotide sequence that is complementary to a firstregion and a second region upstream of exon 7 of the SMN2 pre-mRNA theantisense oligonucleotide sequence is non-sequential, there is a portionof the sequence of the SMN2 pre-mRNA that intervenes between thesequences of the SMN2 pre-mRNA to which the antisense oligonucleotideanneals or is complementary to. That is, the entire sequence of theantisense oligonucleotide is not complementary to a wholly consecutivesequence of the SMN2 pre-mRNA sequence. This is illustrated in FIG. 2,where the entire sequences of v1.00, v1.01, v1.05, v1.06, v1.07, v1.08,v.1.09, v1.10, v1.11, and v1.12 (corresponding to SEQ ID NOs: 6, and11-18), are non-sequential with respect to the SMN2 pre-mRNA, that issplit by intervening sequences of the SMN2 pre-mRNA.

Certain embodiments are drawn to compositions comprising an antisenseoligonucleotide wherein the antisense oligonucleotide comprises, or incertain embodiments consists of, a nucleic acid sequence of SEQ ID NO: 6(v1.00), SEQ ID NO: 7 (v1.01), SEQ ID NO: 8 (v1.02), SEQ ID NO: 9(v1.03), SEQ ID NO: 10 (v1.04), SEQ ID NO: 11 (v1.05), SEQ ID NO: 12(v1.06), SEQ ID NO: 13 (v1.07), SEQ ID NO: 14 (v1.08), SEQ ID NO: 15(v1.09), SEQ ID NO: 16 (v1.10), SEQ ID NO: 17 (v1.11), and SEQ ID NO: 18(v1.12). In certain embodiments, the antisense oligonucleotide sequencecomprises, or in certain embodiments consists of, a nucleic acidsequence comprising one, two, three, four, five, or six nucleotidesubstitutions in the nucleotide sequence of any of SEQ ID NO: 6, SEQ IDNO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ IDNO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQID NO: 17, and SEQ ID NO: 18.

In certain embodiments, any of the antisense oligonucleotides disclosedherein can be a modified nucleotide, such as a Morpholino antisenseoligonucleotide.

Certain embodiments provide for methods of blocking the repressiveactivity of the Element 1 of the SMN2 pre-mRNA wherein the methodcomprises administrating to a subject a composition of the invention.Certain embodiments provide for methods of treating a SMA subject. Incertain embodiments, the method comprises the step of administering to asubject an E1-ASO of an embodiment of the invention. The ability toblock or inhibit the repressive activity of the Element 1 of the SMN2pre-mRNA by an antisense oligonucleotide of the invention is doesdependent. In certain embodiments, the E1-ASO is administered in a doseeffective manner to enhance the level of exon 7-containing SMN2 mRNA incells of the subject. In certain embodiments, the E1-ASO is administeredin an effective amount to treat SMA in a patient. In certainembodiments, the patient is a mammal, such as a human. In certainembodiments, the E1-ASO is a Morpholino modified E1 ASO. One of ordinaryskill in the art would understand that antisense oligonucleotides suchas those described herein, including Morpholino modified nucleic acids,are commercially synthesized and/or otherwise produced by known methods.Intracerebroventricular (ICV), intraperitoneal (IP), and intravenous(IV) administration have been shown to result in increases in SMNprotein. Combinatorial injections have proven to be the mostefficacious. Thus, in certain embodiments, E1 ASOs can be administeredvia ICV, IP, IV, or a combinatorial administration thereof into asubject. In certain embodiments, an antisense oligonucleotide of theinvention is administered via a 1 μM, 2 μM, 3 μM, 4 μM, or 5 μM ICVinjection. In certain methods, a doubling dose is achieved via two ICVinjections or an ICV+IP dosing.

In certain embodiments, the subject is a mammal. In certain embodiments,the subject is a human. In certain embodiments, the subject is a rodentsuch as a mouse or rat, for example, a transgenic mouse such as strainSMAΔ7 and “readthrough” mice (severe and intermediate forms of SMA). Forexample, following treatment, SMA mice showed significant weight gain,ambulated at near normal levels, lived 200 to 600% longer, and exhibitednear-wild type levels of full-length (exon 7 retaining) SMN protein.

The following disclosed embodiments are merely representative of theinvention which may be embodied in various forms. Thus, specificstructural, functional, and procedural details disclosed in thefollowing Examples are not to be interpreted as limiting.

EXAMPLES Example 1

FIG. 3 shows the results of weight gain for SMA mice versus controlswherein the mice were injected with Morpholino antisenseoligonucleotides comprising the nucleotide sequences of SEQ ID NOs: 6-18(E1 V.00 (original) and E1 V.01 to V.12, respectively).

FIG. 4 shows the results of survival for SMA mice versus controlswherein the mice were injected with Morpholino antisenseoligonucleotides comprising the nucleotide sequences of SEQ ID NOs: 6-18(E1 V.00 (original) and V.01 to V.12, respectively).

Example 2

FIG. 5 shows weight gains among E1^(MO)-ASO-v1.00-treated mice (severeform) and controls, showing the weight gained from birth to when a peakweight was reached. There were three control groups as well: 1) Animalsinjected with scrambled MO-ASOs (no binding specificity); 2) Unaffectedhealthy animals (heterozygous); and 3) Untreated SMA animals. As thedata shows, IP injection had a slight improvement effect on weight gain,however, ICV injection alone had a much more significant impact onweight gain. Moreover, when a combination of both types of injectionswas used, the weight gain for the treated animals reaches almost 900% oftheir initial birth weight. Statistical calculations show thesignificance in the Table 1:

TABLE 1 Avg Std Std P value E1 P value P value Treatment WeightsDeviation Error Morph ICV Untreated Scrambled Scrambled 104% 0.351 0.1010.00001072 0.40907992 1.00000000 Untreated 115% 0.233 0.067 0.000015171.00000000 0.40907992 E1 Morph IP 197% 0.265 0.119 0.01520258 0.000011470.00009196 Only E1 Morph 551% 3.031 0.553 1.00000000 0.000015170.00000964 ICV Only E1 Morph 874% 4.412 1.103 0.00343686 0.000000610.00000050 ICV & IP Heterozygous 1380% 1.520 0.439 0.00000000 0.000000000.00000000

FIG. 6 shows the average times taken for animals (treated mice (severeform) and controls) to right themselves. Righting reflex is a motorfunction test performed on animals. Time-To-Right has been previouslyshown to be a sensitive measurement of gross motor function for SMAanimals. In short, animals are placed on their backs and the timerequired to turn upright is measured. Animals that failed to turn in 30seconds are considered failing the test. As shown in FIG. 6,measurements are from day 7 through 25. Healthy (heterozygous) animalscan do this test within 1-5 seconds from day 7 onward. Although the IPinjected animals failed this motor function test, the ICV and also theICV&IP combinatorial injections have an incredible impact on the motorfunctions on the tested animals. After two weeks the ICV injectedanimals righted themselves under 15 seconds and the ICV&IP injectedanimals did so under 10 seconds. By day 20 the ICV&IP injected animalswere turning under 5 seconds.

FIG. 7 shows a comparison of grip strength between treated mice (severeform) and wild heterozygous mice. Grip strength is another motorfunction test to measure muscle functionality; the grip strength test isperformed by placing animals on a device that measures the animal's pull(grip). The test compared the strength of the unaffected heterozygousmice and the MO-ASOs treated SMA animals after ICV&IP injections. 20trials were measured on the days indicated from P25 to P91.

FIG. 8 shows another performance test comparing treated mice and wildmice. In the Roto-Rod performance test, animals are placed on a rotatingaxle, while time is measured for their ability to stay on withoutfalling. In the beginning, treated animals performed exactly like theirhealthy littermates. With time, their strength weakens and theirperformance decreases. Up until around day 45, treated animals performedvirtually as unaffected heterozygous animals.

FIG. 9 shows a comparison of the survival data among treated mice andcontrols. As shown in FIG. 9, the IP only injected animals had a veryslight extension of survival. However, the ICV injected animals reachedan average of 39 days (max. 83 days), whereas, the combinatorial ICV&IPinjections extended the average life span to 54 days (max. 89 days). Theextension of survival of the treated animals demonstrates the clinicpotential of treatment based on ASOs targeting E1.

FIG. 10 shows Western-blot analysis to determine the SMN proteininduction in treated animals (severe form with ICV injections only)compared to controls. Protein induction was significantly higher in alltissues tested with substantial increase in spinal cord and muscletissues. Three separate mice were used to determine the significance inthe protein induction.

FIG. 11 shows protein induction in different types of tissue. As shownin FIG. 11, three quantification graphs of the Western Blots datafurther confirmed the significant increase in protein productionespecially in muscle and spinal cord tissues. The Western Blots analysisfurther proved the viability of the treatment based on the inventiveASOs targeting E1.

The same experimental and testing design was been applied to adifferent, intermediate mouse model (the “Readthrough” mice),representing a milder form of SMA, through the ICV injections only. Thedata on weight gain increases, various motor functionality tests, andaverage protein induction analysis was comparable to that of the treatedsevere-form mice.

FIG. 12( a,b) shows RT-PCR analysis for SMN-full length and SMNΔ7 ontreated mice and controls. As shown in FIG. 12( a,b), the level of exon7-retaining full length SMN increased significantly in the mice treatedwith the inventive Morpholino modified E1 ASOs.

Example 3

A single intracerebroventricular (ICV) injection of E1^(MO)-ASO (Element1 v1.00; SEQ ID NO: 6) in the relatively severe mouse model of SMA(SMNΔ7 mouse model) elicited a robust induction of SMN protein and meanlife span was extended ˜300% following a single dose, consistent withlarge weight gains and a correction of the neuronal pathology.Additionally, E1^(MO)-ASO (Element 1 v1.00; SEQ ID NO: 6) treatment inan intermediate SMA mouse (SMN^(RT) mouse model) significantly extendedlife span by nearly 700% and weight gain was comparable to theunaffected animals. While a number of experimental therapeutics havetargeted the ISS-N1 element of SMN2 pre-mRNA, the development of E1 ASOsprovides a new molecular target for SMA therapeutics that dramaticallyextends survival in two important pre-clinical models of disease.

Materials and Methods Animal Procedures and ASO Delivery

Animals were housed and treated in accordance with Animal Care and UseCommittee guidelines of the University of Missouri, Columbia, Mo., USA.The colony was maintained as heterozygote breeding pairs under specificpathogen free conditions. SMNΔ7 (SMNΔ7^(+/+);SMN2^(+/+);Smn^(−/−)) andSMN^(RT) (SMN^(RT+);SMN2^(+/+);Smn^(−/−)) mice were genotyped on the dayof birth (P1) using standard PCR protocol (JAX® Mice Resources) on tailtissue material. The following primer sets were used: for the mouse Smngene, mSmn-WT forward (5′-tctgtgttcgtgcgtggtgacttt-3′) (SEQ ID NO: 19)and mSmn-WT reverse (5′-cccaccacctaagaaagcctcaat-3′) (SEQ ID NO: 20) andfor the Smn knockout SMN1-KP forward (5′-ccaacttaatcgccttgcagcaca-3′)(SEQ ID NO: 21) and SMN1-KO reverse (5′-aagcgagtggcaacatggaaatcg-3′)(SEQ ID NO: 22). ICV injections were performed on P2, as previouslydescribed (Coady, T. H., et al., 2008; Osman, E. Y., et al., 2012;Passini, M. A., et al., 2011).

Mice were immobilized via cryoanesthesia and injected using μLcalibrated sterilized glass micropipettes. The injection site wasapproximately 0.25 mm lateral to the sagittal suture and 0.50-0.75 mmrostral to the neonatal coronary suture. The needles were insertedperpendicular to the skull surface using a fiber-optic light (BoyceScientific Inc.) to aid in illuminating pertinent anatomical structures.Needles were removed after 10 seconds of discontinuation of plungermovement to prevent backflow. Treated animals were placed in a warmedcontainer for recovery (5-10 minutes) until movement was restored.Single injections of 2 μL of the Morpholino modified E1^(MO)-ASOs weredelivered via intracerebroventricular injections (ICV) as describedabove for all mice. Time-to-right (TTR) reflex tests were conducted aspreviously described (Butchbach, M. E., et al., 2007). Each pup wasplaced onto its back and the time it takes to right itself on the groundwas recorded. The test was terminated at 30 seconds and if an animal hadnot turned by this time, it was recorded as ‘Failure’. Righting reflexmeasurement were recorded daily starting at P7 since unaffected animalsstart to turn over at this time. For grip strength assessment, agrasping response test was utilized. Each pup's front paws were placedon a wire mesh (1 cm² grids) and gently dragged horizontally along themesh (BioSeb Model BP32025, Vitrolles, FR, EU & Pinellas Park, Fla.,USA). Any resistance felt was scored as a positive response. Thestrength of the animal holding onto the mesh before release was recordedin grams. Grip strength was measured every 3-4 days starting on P25.Motor activity and coordination were measured by utilizing rotarodtreadmill for mice (IITC Rotarod Series 8, IITC Life Science Inc., CA,USA). The animals were placed on textured drums to avoid slipping. Whenthe tested animal dropped onto the individual sensing platform below,the test results were recorded in seconds. Measurements were performedevery 3-4 days starting on P25.

Element 1 Antisense Oligonucleotides v1.00 (E1^(MO)-ASO v1.00)

The following oligos were modified at every base with Morpholinochemistry groups (GeneTools L.L.C., Philomath, Oreg. 97370 USA);E1^(MO)-ASO (26-mer) 5′-CUA UAU AUA GAU AGU UAU UCA ACA AA-3′ (SEQ IDNO: 23), and negative scrambled control provided and tested by GeneToolsL.L.C. (25-mer), 5′-CCU CUU ACC UCA GUU ACA AUU UAU A-3′ (SEQ ID NO:24).

Immunohistochemistry of Neuromuscular Junctions (NMJs)

Immunochemistry and NMJ analysis were performed following a modifiedprotocol described in detail previously (Cobb, M. S., et al., 2013;Ling, K. K., et al., 2012). Three animals from each treatment andcontrol groups at age P12 were anaesthetized by anesthetic inhalantIsoflurane® USP, VetOne™ (1-chloro-2,2,2-trifluoroethyl difluoromethylether; 50 mg/kg) followed by transcardiac perfusion with PhosphateBuffered Saline (PBS) solution (Dulbecco's, Gibco®, LifeTechnologies™Carlsbad, Calif., USA), and fixed with 4% paraformaldehyde(Sigma-Aldrich, St. Louis, Mo., USA). Whole-mount preparations were doneby dissecting and examining the longissimus capitis muscle. Tissues werestained using specific antibodies including anti-neurofilament (1:2000;Chemicon®, EMD Millipore, Billerica, Mass., USA) and anti-synaptophysin(1:200, LifeTechnologies™ Carlsbad, Calif., USA). Acetylcholinereceptors (AChRs) were labeled with Alexa Fluor 594-conjugatedα-bungarotoxin (LifeTechnologies™ Carlsbad, Calif., USA). Musclepreparations were viewed using a laser scanning confocal microscope (40×objective; 0.8NA; Zeiss LSM Model 510 META, Carl Zeiss, Jena, Germany,EU). From the confocal microscopy, Z-series stack images ofimmunostained whole-mount muscles were obtained at sequential focalplanes 1 μm apart and merged using microscope integrated software anddespeckled by ImageJ software, Fiji (Schindelin, J., et al., 2012).

RT-PCR Assays

Total RNA was isolated from brain tissues harvested on P7 andhomogenized using TRIzol reagent (LifeTechnologies™ Carlsbad, Calif.,USA). Two micrograms of total RNA was used to generate first-strand cDNAby using 100 ng of random primers, 2 microliters dNTP (10 mM) Mix; 4microliters of 5× first-strand buffer, 1.0 microliter DTT (0.1 M) and1.0 microliter SuperScript™ III Reverse Transcriptase (200 U permicroliter) (LifeTechnologies™ Carlsbad, Calif., USA) at 50° C./50 minfollowed by reaction inactivation at 70° C./15 min. Cycling conditionswere as follows: an initial denaturation step (94° C./3 min), 30 cycles(94° C./30 sec; 60° C./0.5 min; 72° C./1 min), and a final extensionstep (72° C./10 min). Reaction products were resolved by electrophoresisthrough a 2.0% agarose gel (GeneMate, BioExpress, Kaysville, Utah, USA)and visualized by ethidium bromide staining on FOTODYNE™ Imaging Systems(Hartland, Wis., USA). For cDNA controls specific plasmids pCIExSkip andpCIFL were used (Lorson, C. L., et al., 1999).

Western Blots

For the SMNΔ7 mouse Western blots, indicated tissues were collected atselected time points (P7) and immediately frozen in liquid nitrogen.Tissue samples were placed at −80° C. until ready for analysis. Roughly100 mg of tissue was homogenized in JLB buffer (50 mM Tris-HCl pH 7.5,150 mM NaCl, 20 mM NaH₂(PO₄), 25 mM NaF, 2 mM EDTA, 10% glycerol, 1%Triton X100, and protease inhibitors (Roche, Indianapolis, Ind., USA)).Equal amounts of protein were separated on 12% SDS-PAGE gels. SMNimmunoblots were performed using a mouse SMN specific monoclonalantibody (BD Biosciences, San Jose, Calif., USA) diluted 1:300 in TBST(Tris-buffered Saline Tween20 (10 mM Tris-HCl, pH7.5, 150 mM NaCl, 0.2%Tween20)) in 1.5% dry milk. Then blots were visualized bychemiluminescence on a Fujifilm imager LAS-3000 (FujiFilm^(USA), HanoverPark, Ill., USA) and the corresponding software. To verify equal loadingthe Westerns were then stripped using H₂O₂ for 30 minutes at roomtemperature and re-probed with anti-β-actin rabbit and anti-rabbit HRPsecondary antibody (Jackson ImmunoResearch Laboratories, Inc. WestGrove, Pa., USA). Western blots were performed in quadruplicate or moreand representative blots are shown.

Results

FIG. 13 illustrates targeting of the intronic repressor Element 1 withmorpholino modified ASOs. FIG. 13 is a schematic representation ofspecific morpholino-modified ASO targeting the intronic repressorElement 1 (E1^(MO)-ASO). A specific design of an E1^(MO)-ASO isillustrated with the antisense domains consisting of two non-sequentialtarget antisense sequences targeting the intronic Element 1 repressor.In addition, several previously published ASO sequences with differentmodified chemistries and targeting the intronic silencer ISS-N1 are alsoshown.

FIG. 14 shows an increase in full-length SMN transcript afterE1^(MO)-ASO treatment. RT-PCR image showing full-length SMN in threeindividual animals. The plasmids pCIExSkip and pCIFL were used for cDNAcontrols.

FIG. 15 shows that injection of morpholino based ASO targeting theElement1 repressor increased total SMN protein in the Δ7SMA mouse model.Single ICV injection of E1^(MO)-ASO increase SMN protein levels. Westernblots (n=5) for each treatment group were performed on brain, spinalcord and muscle tissues at P7.

FIG. 16 a shows that severe SMNΔ7 SMA mice showed significantimprovement in survival and longevity after injections with E1^(MO)-ASOoligos. Kaplan-Meier survival curves were constructed from the varioustreatment groups and the routes of delivery as indicated. Log-rank(Mantel-Cox) statistics were applied for comparisons between groupswhere p<0.0001 for all treatment groups compared to untreated animals,with the exception of E1^(MO)-ASO IP injected animals when compared tothe untreated controls (p=0.0526). FIG. 16 b shows survival curvesdemonstrating a significant increase in life expectancy for E1^(MO)-ASOICV, ICV&ICV and ICV&IP injected animals with increases in mediansurvival to 39, 54 and 54 days respectively. Some tail necrosis wasdisplayed by the ICV injected SMA animals around day 40-45 (not shown).

FIG. 17 shows that E1^(MO)-ASO treatment results in a significant weightgain. Referring to FIG. 17, starting at P7, E1^(MO)-ASO injected animalswere heavier than untreated, scrambled and IP only injected SMAcontrols. Total body weight was measured daily for all animal groupspost injection.

FIG. 18 a shows the percent weight gained from birth to peak was alsocompared between groups treated. FIG. 18 b shows statisticalsignificance between each treatment group. Statistical significance inpercent weight gain from birth to peak after E1^(MO)-ASO treatment.P-values are shown for each treatment group. Student's t-Test was usedto compare each group against all treatment and control animals. Pvalues were rounded to the sixth decimal point.

FIG. 19 shows individual weights on P12 for all controls and animalstreated with E1^(MO)-ASO.

FIG. 20 is a bar graph showing the percent of all tested animal groupsable to right themselves from a prone position. By P14, more than fiftypercent of all ICV, ICV&ICV, and ICV&IP injected were able to rightthemselves.

FIG. 21 a is a graph representing raw data of the average time to rightfrom P7 to P25. Animals injected with E1^(MO)-ASO ICV, E1^(MO)-ASOICV&ICV and E1^(MO)-ASO ICV&IP were able to right themselves within 20seconds after 2 weeks. FIG. 21 b is a scatter plot of TTR performance ofmice injected with E1^(MO)-ASO. To highlight the performance ofindividual mice, TTR values are shown for P12.

FIG. 22 shows grip strength measurements in grams. Treated animals werecompared to their unaffected littermates. Measurements were taken fromP25 through P77.

FIG. 23 shows results of the rotarod performance test. The test was usedto measure riding time parameter (in seconds) of the E1^(MO)-ASO treatedanimals and compared with the times of their age-matched unaffectedcontrols. Measurements were taken from P25 through P77.

Improvement in neuromuscular junctions (NMJs) pathology. The longissimuscapitis (LC) muscles from ICV injected and control animals at P12 wereimmunostained for nerve terminals withanti-neurofilament/anti-synaptophysin [Nerve/Syn] and motor endplateswith α-bungarotoxin. While the untreated SMNΔ7 mice displayed typicalsevere denervation, E1^(MO)-ASO treatment substantially restored NMJ'spretzel-like structures (not shown).

SMN protein induction in the milder mouse model of SMA (SMN^(RT)). FIG.24 a is a Western blot (n=3) showing increased SMN in spinal cord tissueof five (5) ICV injected animals with E1^(MO)-ASO. FIG. 24 b showsWestern blot quantification. Bar graph showing no significant differencein protein induction between unaffected and treated milder type SMA^(RT)mice.

SMN^(RT) mice injected with E1^(MO)-ASO, showed significant improvementin survival and weight gain. FIG. 25 shows that the treated SMN^(RT)animals (labeled “SMN^(RT) E1^(MO)-ASO”) and the unaffected littermates(labeled “SMN^(RT) Unaffected”) were substantially more vigorous andlived more than 180 days compared to the untreated mice (labeled“SMA^(RT) Untreated”). The Kaplan-Meier survival curve depicts anidentical in life expectancy for unaffected and treated SMN^(RT) mice.Animals were culled after 180 days.

FIG. 26 shows a significant increase in the average weight of SMN^(RT)animal model after treatment with E1^(MO)-ASO.

FIG. 27 show a comparison of the percent weight gained from birth topeak between animal groups. For statistical significance between eachtreatment group, Student's T-Test was used and p-values are shown forE1^(MO)-ASO SMN^(RT) animals.

FIG. 28 shows individual weights on P12. Weights of treated mice arecomparable to the weights of unaffected age-matched littermates.

TTR, muscle strength, balance, and motor-planning measurements showsignificant improvement in E1^(MO)-ASO treated SMN^(RT) mice. FIG. 29shows the percent of the tested animals able to right themselvescompared to untreated mice where the TTR reflex is delayed. By P9, alltreated and unaffected animals were able to right themselves.

FIG. 30 shows the average time to right from P7 to P25 for allexperimental groups. SMN^(RT) mice injected with E1^(MO)-ASO were ableto right themselves within 10 seconds after 10 days.

FIG. 31 is a scatter plot of TTR performance of SMN^(RT) mice injectedwith E1^(MO)-ASO. Time-to-right performance of individual mice at ageP12 shows that treated animals can successfully turn themselves within 5seconds.

FIG. 32 shows grip strength measurements in grams. Treated animals werecompared to their unaffected littermates. Measurements were taken fromP25 through P108.

FIG. 33 shows results of the rotarod performance test. The test was usedto measure riding time parameter (in seconds) of the E1^(MO)-ASO treatedanimals and compared with the times of their age-matched unaffectedcontrols. Measurements were taken from P26 through P110.

FIG. 34 is RT-PCR quantification showing the percent increase in fulllength SMN transcript in three SMA animals after treatment withE1^(MO)-ASO.

FIG. 35 is Western blot quantification showing the percent increase inSMN protein induction was compared to the unaffected and untreatedcontrol group and plotted in a bar graph. (n=5).

Delayed tail necrosis in E1^(MO)-ASO ICV/IP injected animals. Afterdelivery via the combinatorial routes of ICV and IP injections, thetreated animals exhibited a delayed tail necrosis (day 60-65) (notshown). E1^(MO)-ASO ICV injected SMN^(RT) animals were indistinguishablefrom their unaffected littermates in movement and behavior pattern.Necropsy of male SMN^(RT) mouse treated with E1^(MO)-ASO at age 175 daysshowed significant internal organ abnormalities such as deformed heart,subcutaneous fluid retention, and smaller kidneys. Enlarged and swollenbladder were clearly evident (not shown).

Element 1 as an ASO Target

To expand the repertoire of potential targets for SMA therapeutics,Morpholino-modified ASOs (E1^(MO)-ASOs) were developed that target theE1 repressor, a region distinct from the ISS-N1 repressor which has beenthe focus of the overwhelming majority of ASO strategies (FIG. 13).

Following a single injection into the central nervous system viaintracerebroventricular (ICV) delivery of the E1^(MO)-ASO, pre-mRNAexon-skipping from the SMN2 transgene was significantly reduced in totalRNA isolated from brain tissue, resulting in a nearly 3-4 fold increasein full-length SMN transcript in each of three animals examined.

FIG. 14 shows the increase in full-length SMN transcript afterE1^(MO)-ASO treatment. RT-PCR image showing full-length SMN in threeindividual animals. The plasmids, pCIExSkip and pCIFL, were used forcDNA controls.

The mice used in this experiment were phenotypically wild type(unaffected), but carried the human genomic SMN2 gene. To determine ifSMN levels increased similarly, a single ICV injection was delivered toSMNΔ7 (SMNΔ7^(+/+);SMN2^(+/+);Smn^(−/−)) pups on P2 and protein extractswere collected from brain, spinal cord, and skeletal muscle (Musculusgastrocnemius). The SMNΔ7 model, which has an average life span of 12-14days, has been extensively characterized and utilized for a number oftranslational studies (Le, T. T., et al., 2005; Osborne, M. and Lutz,C., 2013; Lorson, M. A. and Lorson, C. L., 2012). In each treated animalexamined, SMN protein levels were elevated several fold compared tountreated SMA animals, although wildtype tissue still contained slightlyhigher levels of SMN.

Phenotypic Correction in Severe SMA Mice

To determine whether delivery of the E1^(MO)-ASO to SMA mice on P2improved the phenotype; survival, weight gain, righting reflexes andstrength measurements were collected. A relatively low dose (2 mM) ofASO was selected, comparable to the “low” dose from a previouslypublished report examining ISS-N1 ASOs (Porensky, P. N., et al., 2012).Untreated SMA mice lived less than 2 weeks, similar to a cohort treatedwith a control ASO consisting of the scrambled sequence. Similarly,delivery of the E1^(MO)-ASO via a single intraperitoneal (IP) injectionfailed to extend survival beyond 1-2 days. However, a single ICVinjection of E1^(MO)-ASO led to nearly a 400% improvement in life span,with more than one third of the treated animals living beyond 50 days.When we looked at the life span of the negative control group animals,we observed no difference between our untreated and the scrambledMorpholino injected animals. SMA animal models exhibit extensiveperipheral defects, particularly in severe models. To determine whetherE1^(MO)-ASO treatment would rescue peripheral defects, a combinatorialtreatment of ICV and IP injections was performed: two injections of the2 mM ASO were delivered via ICV and an IP injection. In a separatecohort, two ICV injections were administered separated by 12 hours. Thedouble-dosing resulted in a similar extension in survival, out to anaverage of 54 days, with more than one quarter of the animals livingbeyond 70 days. While the treated mice were highly ambulatory, distalnecrosis, particularly of the tail, was observed in nearly all of thelonger lived animals. In the ICV treated cohort, necrosis initiated atapproximately P40-45, while ICV/IP treatment delayed necrosis onset toapproximately P60. Collectively, these results demonstrate that theE1^(MO)-ASO can significantly extend survival in a severe mouse model ofSMA.

E1^(MO)-ASO treatment resulted in significant weight gain compared toeither untreated, scramble or IP-only ASO treated cohorts. The ICV/IPtreated animals gained the most weight compared to the ICV or ICV/ICVgroups, resulting in animals that achieved 15-18 grams. This was instark contrast to the untreated, scramble or IP-only ASO treated cohortsthat failed to thrive and were unable to achieve 5 grams. An additionalmeasure of phenotypic correction used in the SMA field is thetimed-righting response. Animals are placed on their backs and the timeit takes to stand on four legs is recorded, as well as failed attempts.In the ICV, ICV/ICV, and ICV/IP cohorts, SMA treated animals improvedsignificantly based upon the percentage of animals that couldsuccessfully turn over as well as the speed at which the animalssuccessfully righted themselves.

Typically, SMA animals do not live long enough to perform gross motorfunction tests such as rotarod and grip strength; however, E1^(MO)-ASOtreated mice lived long enough and were healthy enough to perform theseassays. Following a one week period to acclimate to the equipment, gripstrength and rotarod performance was collected for 16 consecutive days.Grip strength analysis revealed that the SMA E1^(MO)-ASO treated animalsperformed consistently, albeit with less force, compared to wild typeanimals. Rotarod performance also demonstrated that the ASO-rescuedanimals were not fully corrected compared to wild type animalsespecially at later time points. While the treated animals were neverfully corrected compared to wild type animals, it is important to stressthat their untreated (or scramble-treated cohorts) were dead weeks priorto these studies. This increasing discrepancy could in part be due tothe development of tail necrosis as flexibility and/or loss of the tailwould impact balance and rotarod performance.

An important hallmark of the SMA phenotype that directly relates todisease pathogenesis is the integrity of the neuromuscular junctions(NMJs). As expected, NMJs from untreated SMA mice appear immature,poorly developed and there was little overlap between the pre- andpost-synaptic endplate. In contrast, the wild type andE1^(MO)-ASO-treated tissues exhibit well developed NMJs with a highdegree of connectivity between the axons and the post-synaptic endplate.These results are consistent with the significant correction of the SMAphenotype at the organismal level and provide evidence that a molecularcorrection of SMN2 splicing using an E1^(MO)-ASO can profoundly reversethe severe SMA phenotype observed in SMNΔ7 mice.

Phenotypic Correction in Intermediate SMA Mice

Testing therapeutics in more than one model of disease validates themolecular engagement of a specific target, demonstrates applicability toa broader range of the patient population, and sheds light upon thebiology of the disease. To address these important parameters, a newlydeveloped intermediate model of disease was examined. This model,SMN^(RT), expresses low levels of SMN, lives approximately 32 days, andexhibits an intermediate phenotype in most cellular and organismalparameters of disease (Cobb, M. S., et al., 2013). Following a singleICV injection of the E1^(MO)-ASO (2 mM), SMN protein was increasedsignificantly, approximately 8-10 fold above untreated levels in spinalcord extracts. To verify whether ICV delivery of E1^(MO)-ASO alsoextended survival of the milder form SMA animals, lifespan for thetreatment groups were analyzed by Kaplan-Meier survival curve andcompared to the lifespan of the animals from the control groups. ICVinjections of the E1^(MO)-ASO significantly increased the averagelifespan of the SMN^(RT) mice, compared to their aged-matched untreatedcontrol animals. In fact, all E1^(MO)-ASO treated animals were stillalive at P175, at which point the experiment was stopped and animalswere euthanized. The treated SMN^(RT) mice were phenotypicallyindistinguishable from their unaffected age-matched littermates withinthe first two months of their life span. Consistent with an early androbust increase of SMN, treated SMN^(RT) mice gained weight to near wildtype levels during the first 4-5 weeks, and treated animals weighed asmuch as wild type animals beyond approximately 40 days. At nearly alltime points, SMN^(RT) treated mice were able to right themselves morerapidly than untreated mice and were as efficient as the wild typeanimals at time points beyond P10. Differences in grip strength androtarod performance were detected over the trial period and as theanimals aged, a greater disparity was observed between SMN^(RT) treatedmice and unaffected animals. Similar to the SMNΔ7 experiments, theinitiation of tail necrosis later in life (at approximately P70-80 forthe SMN^(RT) mice) may have negatively impacted their ability to performin these assays.

The dose that was initially administered was a 2 μM ICV injection.However, a doubling of this dose via two ICV injections or an ICV+IPdosing further enhanced survival. Interestingly, the ICV+IP dosing wasthe most efficacious presumably because the IP administration allowedfor a greater distribution to peripheral tissues. It is also importantto stress that the SMA mouse models do not necessarily reflect thefrequency of peripheral complications in most SMA patients. Currently,all of the SMA models exhibit profound peripheral organ defects, whileperipheral organ damage in SMA patients is largely restricted to verysevere SMA cases.

While the invention has been described in connection with specificembodiments thereof, it will be understood that the inventive device iscapable of further modifications. This patent application is intended tocover any variations, uses, or adaptations of the invention following,in general, the principles of the invention and including suchdepartures from the present disclosure as come within known or customarypractice within the art to which the invention pertains and as may beapplied to the essential features herein before set forth.

What claimed is:
 1. A composition for blocking the repressive activityof the Element 1 of the SMN2 pre-mRNA, the composition comprising anantisense oligonucleotide that comprises a sequence annealing to a firstregion and a second region of the SMN2 pre-mRNA, wherein the firstregion of the SMN2 pre-mRNA consists of the nucleotides between −134 to−90 relative to exon 7 of the SMN2 pre-mRNA and the second region of theSMN2 pre-mRNA consists of the nucleotides between −105 to −45 relativeto exon 7 of the SMN2 pre-mRNA.
 2. The composition of claim 1 whereinsaid antisense oligonucleotide comprises a Morpholino backbone.
 3. Thecomposition of claim 1 wherein the antisense oligonucleotide comprises anucleic acid sequence selected from the group consisting of SEQ ID NO:17 (v1.11), SEQ ID NO: 16 (v1.10), SEQ ID NO: 6 (v1.00), SEQ ID NO: 7(v1.01), SEQ ID NO: 8 (v1.02), SEQ ID NO: 9 (v1.03), SEQ ID NO: 10(v1.04), SEQ ID NO: 11 (v1.05), SEQ ID NO: 12 (v1.06), SEQ ID NO: 13(v1.07), SEQ ID NO: 14 (v1.08). SEQ ID NO: 15 (v1.09), and SEQ ID NO: 18(v1.12).
 4. The composition of claim 3 wherein said antisenseoligonucleotide comprises a Morpholino backbone.
 5. The composition ofclaim 1 wherein the antisense oligonucleotide comprises a nucleotidesequence that is complementary to at least eight consecutive nucleotidesof the first region of the SMN2 pre-mRNA and is complementary to atleast eight consecutive nucleotides of the second region of the SMN2pre-mRNA, wherein the sequence of the antisense oligonucleotide that iscomplementary to the second region of the SMN2 pre-mRNA is 5′ of thesequence of the antisense nucleotide that is complementary to the firstregion of the SMN2 pre-mRNA.
 6. The composition of claim 5 wherein saidantisense oligonucleotide comprises a Morpholino backbone.
 7. Thecomposition of claim 1 wherein the antisense oligonucleotide comprises:i. a nucleotide sequence that is complementary to, except for having oneor two nucleotide substitutions, at least eight consecutive nucleotidesof the first region of the SMN2 pre-mRNA and is complementary to atleast eight consecutive nucleotides of the second region of the SMN2pre-mRNA; ii. a nucleotide sequence that is complementary to at leasteight consecutive nucleotides of the first region of the SMN2 pre-mRNAand that is complementary, except for having one or two nucleotidesubstitutions, to at least eight consecutive nucleotides of the secondregion of the SMN2 pre-mRNA; or iii. a nucleotide sequence that iscomplementary to, except for having one or two nucleotide substitutions,at least eight consecutive nucleotides of the first region of the SMN2pre-mRNA and that is complementary, except for having one or twonucleotide substitutions, to at least eight consecutive nucleotides ofthe second region of the SMN2 pre-mRNA.
 8. The composition of claim 7wherein said antisense oligonucleotide comprises a Morpholino backbone.9. The composition of claim 5 wherein the entire sequence of theantisense oligonucleotide is not complementary to a wholly consecutivesequence of the SMN2 pre-mRNA sequence.
 10. The composition of claim 9wherein said antisense oligonucleotide comprises a Morpholino backbone.11. The composition of claim 9 wherein the antisense oligonucleotidecomprises a nucleic acid sequence selected from the group consisting ofSEQ ID NO: 17 (v1.11), SEQ ID NO: 16 (v1.10), SEQ ID NO: 6 (v1.00), SEQID NO: 7 (v1.01), SEQ ID NO: 11 (v1.05), SEQ ID NO: 12 (v1.06), SEQ IDNO: 13 (v1.07), SEQ ID NO: 14 (v1.08). SEQ ID NO: 15 (v1.09), and SEQ IDNO: 18 (v1.12).
 12. The composition of claim 11 wherein said antisenseoligonucleotide comprises a Morpholino backbone.
 13. The composition ofclaim 7 wherein the entire sequence of the antisense oligonucleotide isnot complementary to a wholly consecutive sequence of the SMN2 pre-mRNAsequence.
 14. The composition of claim 13 wherein said antisenseoligonucleotide comprises a Morpholino backbone.
 15. A method forblocking the repressive activity of the Element 1 of the SMN2 pre-mRNA,the method comprising the step of administrating to a subject thecomposition of any of claims 1 to
 14. 16. The method of claim 15 whereinthe composition is administered intracerebroventricularly,intraperitoneally, intravenously, or by a combinatorial administrationthereof.
 17. A method for treating Spinal Muscular Atrophy (SMA) in ahuman SMA patient, the method comprising the step of administrating tothe patient an effective amount of a composition of any of claims 1 to14.
 18. The method of claim 17 wherein the composition is administeredintracerebroventricularly, intraperitoneally, intravenously, or by acombinatorial administration thereof.
 19. A composition for blocking therepressive activity of the Element 1 of the SMN2 pre-mRNA, thecompositions comprising an antisense oligonucleotide with a sequenceannealing to a first region and a second region of the SMN2 pre-mRNA,wherein the first region consists of the nucleotides between −134 to−120 relative to exon 7 of the SMN2 pre-mRNA and the second regionconsists of the nucleotides between −67 to −54 relative to exon 7 of theSMN2 pre-mRNA.
 20. The composition of claim 19 wherein said antisenseoligonucleotide comprises a Morpholino backbone.
 21. A method forblocking the repressive activity of the Element 1 of the SMN2 pre-mRNA,thereby modulating the splicing pattern of the SMN2 to generatefull-length (exon-7-retaining) SMN comprising the step of administratingto a subject a composition comprising an antisense nucleotide with asequence annealing to two distinct regions flanking E1 on the SMN2pre-mRNA, whereas the regions consist of the nucleotides between −134 to−120 and −67 to −54 (relative to exon 7) and a Morpholino backbone.